title: Nucleic acid secondary structures containing the double-headed nucleoside 5'(S)-C-(2-(thymin-1-yl)ethyl)thymidine.
abstract: Oligodeoxynucleotides containing the double-headed nucleoside 5'(S)-C-(2-(thymin-1-yl)ethyl)thymidine were prepared by standard solid phase synthesis. The synthetic building block for incorporating the double-headed moiety was prepared from thymidine, which was stereoselectively converted to a protected 5'(S)-C-hydroxyethyl derivative and used to alkylate the additional thymine by a Mitsunobu reaction. The oligodeoxynucleotides were studied in different nucleic acid secondary structures: duplexes, bulged duplexes, three-way junctions and artificial DNA zipper motifs. The thermal stability of these complexes was studied, demonstrating an almost uniform thermal penalty of incorporating one double-headed nucleoside moiety into a duplex or a bulged duplex, comparable to the effects of the previously reported double-headed nucleoside 5'(S)-C-(thymin-1-yl)methylthymidine. The additional base showed only very small effects when incorporated into DNA or RNA three-way junctions. The various DNA zipper arrangements indicated that extending the linker from methylene to ethylene almost completely removed the selective minor groove base-base stacking interactions observed for the methylene linker in a (-3)-zipper, whereas interactions, although somewhat smaller, were observed for the ethylene linker in a (-4)-zipper motif.
authors.affiliation: Nucleic Acid Center, Department of Chemistry and Physics, University of Southern Denmark, 5230 Odense M, Denmark.
authors.forename: Charlotte
authors.initials: C
authors.lastname: Andersen
authors.forename: Pawan K
authors.initials: PK
authors.lastname: Sharma
authors.forename: Mikkel S
authors.initials: MS
authors.lastname: Christensen
authors.forename: Signe I
authors.initials: SI
authors.lastname: Steffansen
authors.forename: Charlotte M
authors.initials: CM
authors.lastname: Madsen
authors.forename: Poul
authors.initials: P
authors.lastname: Nielsen
mesh_terms: D001483:Base Sequence; D002244:Carbon / Q000737:chemistry; D009690:Nucleic Acid Conformation; D009696:Nucleic Acids / Q000737:chemistry* / Q000235:genetics; D009838:Oligodeoxyribonucleotides / Q000737:chemistry / Q000235:genetics; D013936:Thymidine / Q000031:analogs & derivatives* / Q000138:chemical synthesis
chemical_list: C521750:5'(S)-C-(thymine-1-ylmethyl)thymidine; D009696:Nucleic Acids; D009838:Oligodeoxyribonucleotides; D002244:Carbon; D013936:Thymidine